N silico molecular characterization of a putative haloacid dehalogenase type ii from genomic of mesorhizobium loti strain tono

• Main Authors: Zakary, Sefatullah, Mashal, Hamida, Osmani, Abdul Rahman, Oyewus, Habeebat Adekilekun, Huyop, Fahrul, Mohammad Nasim, Muzhgan
• Format: Article
• Published: Brawijaya University 2022
• Subjects: Q Science (General)
• Online Access: http://eprints.utm.my/id/eprint/98777/; http://dx.doi.org/10.11594/jtls.12.02.10
• Institution: Universiti Teknologi Malaysia

Halogenated organic compounds are found as waste in the biosphere and can cause numerous dilemmas because of their toxicity and persistence in the environment. They play a major role in the quality of life of both, human beings and other living organisms. Degradation of these compounds by microorganisms is significant to reduce recalcitrant and cost. Thus, in the current study, an in-silico approach was used for homology modelling and docking assessment of a newly identified DehLt4, type II dehalogenase to predict its ability to degrade selected haloalkanoic acids and haloacetates. The study aimed to establish the catalytic tendencies of the enzyme to optimally degrade the selected halogenated haloacids. The refined modelled structure of DehLt4 using GROMACS 5.1.2 software revealed satisfactory scores of ERRAT (94.73%), Verify3D (90.83%) and PROCHECK (99.05 %) assessments. Active site prediction by blind docking and multiple sequence alignment indicated the catalytic triads for DehLt4 were Asp9-Lys149-Asn175. Both L-2-chloropropionic acid (L-2-CP) and trichloroacetate (TCA) docked with DehLt4 exhibited binding energy of -3.9 kcal/mol. However, the binding energy for D-2-chloropropionic acid (D-2-CP) and monochloroacetate (MCA) was -3.8 kcal/mol and -3.1 kcal/mol, respectively. Thus, the findings of the study successfully identified the catalytic important residues of DehLt4 for possible pollutant degradation. The in-silico study as such has a good potential for characterization of newly identified dehalogenases based on basic molecular structure and functions analysis.